A mixed incoherent feed-forward loop contributes to the regulation of bacterial photosynthesis genes.

Mank NN, Berghoff BA, Klug G - RNA Biol (2013)

Bottom Line:
Living cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes.In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand.This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.

ABSTRACTLiving cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes. In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand. Recently, we identified a mixed incoherent feed-forward loop comprising the transcription factor PrrA, the sRNA PcrZ and photosynthesis target genes as part of this regulatory network. This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.

Mentions:
Bacterial small RNAs (sRNAs) are widely recognized as important regulators of gene expression and commonly operate at the post-transcriptional level by influencing mRNA stability and/or translation.1,2 The combination of transcriptional and post-transcriptional gene control by protein transcription factors and sRNAs, respectively, endues bacteria with elaborate switches for adaptive processes. Examples for regulatory networks consisting of transcription factors and sRNAs, which either concertedly control genes or regulate each other, are accumulating; sRNAs extend the regulatory scope of the networks and alter their dynamics.3 The combined networks are frequently employed by bacteria to adapt to sudden changes, such as upcoming stress factors or changes in nutrient availability. Especially bacteria living in quickly alternating environments have a need for sophisticated fine-tuning of gene regulation. In the case of purple bacteria like Rhodobacter, the amount of photosynthetic complexes is adjusted to the given oxygen tension and light intensities by a complex network of protein factors (Fig. 1).4,5 For example, the response regulator PrrA activates transcription of photosynthesis genes when oxygen tension drops. However, it was recently shown that the trans-encoded sRNA PcrZ (photosynthesis control RNA Z) of Rhodobacter sphaeroides is transcribed from a PrrA-dependent promoter and subsequently counteracts the induction of photosynthesis genes on the post-transcriptional level.6 This regulatory interplay constitutes a rare example of a mixed incoherent feed-forward loop (FFL) involving a protein regulator (PrrA) and an sRNA (PcrZ), which finally allows for balanced expression of photosynthetic complexes. In this point-of-view, we will compare expression kinetics of PcrZ with those of photosynthesis genes and draw a comparison to other described FFLs. The physiological relevance of PcrZ will be discussed in detail.

Mentions:
Bacterial small RNAs (sRNAs) are widely recognized as important regulators of gene expression and commonly operate at the post-transcriptional level by influencing mRNA stability and/or translation.1,2 The combination of transcriptional and post-transcriptional gene control by protein transcription factors and sRNAs, respectively, endues bacteria with elaborate switches for adaptive processes. Examples for regulatory networks consisting of transcription factors and sRNAs, which either concertedly control genes or regulate each other, are accumulating; sRNAs extend the regulatory scope of the networks and alter their dynamics.3 The combined networks are frequently employed by bacteria to adapt to sudden changes, such as upcoming stress factors or changes in nutrient availability. Especially bacteria living in quickly alternating environments have a need for sophisticated fine-tuning of gene regulation. In the case of purple bacteria like Rhodobacter, the amount of photosynthetic complexes is adjusted to the given oxygen tension and light intensities by a complex network of protein factors (Fig. 1).4,5 For example, the response regulator PrrA activates transcription of photosynthesis genes when oxygen tension drops. However, it was recently shown that the trans-encoded sRNA PcrZ (photosynthesis control RNA Z) of Rhodobacter sphaeroides is transcribed from a PrrA-dependent promoter and subsequently counteracts the induction of photosynthesis genes on the post-transcriptional level.6 This regulatory interplay constitutes a rare example of a mixed incoherent feed-forward loop (FFL) involving a protein regulator (PrrA) and an sRNA (PcrZ), which finally allows for balanced expression of photosynthetic complexes. In this point-of-view, we will compare expression kinetics of PcrZ with those of photosynthesis genes and draw a comparison to other described FFLs. The physiological relevance of PcrZ will be discussed in detail.

Bottom Line:
Living cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes.In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand.This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.

ABSTRACTLiving cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes. In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand. Recently, we identified a mixed incoherent feed-forward loop comprising the transcription factor PrrA, the sRNA PcrZ and photosynthesis target genes as part of this regulatory network. This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.